gp_overview: gp_overview

In polymapR: Linkage Analysis in Outcrossing Polyploids

gp_overview

Description

Function to generate an overview of genotype probabilities across a population

Usage

gp_overview(probgeno_df, cutoff = 0.7, alpha = 0.1)

Arguments

probgeno_df	A data frame as read from the scores file produced by function saveMarkerModels of R package fitPoly, or equivalently, a data frame containing the following columns: SampleName Name of the sample (individual) MarkerName Name of the marker P0 Probabilities of dosage score '0' P1... Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population) maxP Maximum genotype probability identified for a particular individual and marker combination maxgeno Most probable dosage for a particular individual and marker combination geno Most probable dosage for a particular individual and marker combination, if maxP exceeds a user-defined threshold (e.g. 0.9), otherwise NA
cutoff	a filtering threshold, by default 0.7, to identify individuals with more than alpha non-missing (maximum) genotype probabilities falling below this cut-off. In other words, by using this default settings (cutoff = 0.7 and alpha = 0.1), you require that 90 in one of the possible genotype dosage classes. This can help identify problematic individuals with many examples of diffuse genotype calls. Lowering the threshold allows more diffuse calls to be accepted.
alpha	Option to specify the quantile of an individuals' scores that will be used to test against cutoff, by default 0.1.

Value

a list with the following elements:

probgeno_df

Input data, filtered based on chosen cutoff

population_overview

data.frame containing summary statistics of each individual's genotyping scores

Examples

## Not run: 
data("gp_df")
gp_overview(gp_df)

## End(Not run)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.